Selecting an organism

When you are on the Datasets top menu in the BTK viewer, you can either click on taxa in the taxonomy tree, and go deeper till you find your species of interest, or you can type its scientific name or common name in the search box.

For our first example, we’re going to try both approaches to find a plant pathogen fungus called Didymella arachidicola, which causes leaf blotch of peanut plants in Africa and Asia.

1. Tree based

On the very left you see Eukaryota followed by some numbers. It is shown expanded into 4 major kingdoms: Fungi (eg mushrooms), Metazoa (animals), Viridiplantae (plants), and Other Eukaryota (eg Protists, Apicomplexa, etc). If you click on the name, eg Fungi, the viewer will show you ALL genome assemblies available under that high level taxon group in a table. However, if you click on the numbers to the right of the name, it will expand the tree further.

The numbers (eg for Fungi, it says 4466/6697) indicate that 4466 fungi species have BTK views available out of the total number of fungi species in the public archives. In an ideal world we would have the same number for both but in reality, new species get added all the time, so not all public genome assemblies have BTK views available.

Genome assemblies are considered public when they are available and indexed in the International Nucleotide Sequence Database Collaboration (INSDC) archives such as the American NCBI GenBank, European EBI ENA, and Japanese DDBJ. If someone puts a genome assembly in a publicly accessible place like zenodo.org, or on a website, or even as part of supplemental materials for a paper – then yes, it is “available” but it is not indexed and accessioned in a way that everyone can find it easily.

For now, let’s use the browser to click on the the numbers next to the taxon name to expand the tree:

Fungi > Ascomycota > Dothideomycetes > Pleosporales > Didymellaceae > Didymella. At this point you should see all 6 species in the public archives and the tree cannot be expanded any further.

Click to expand

The colours in the tree tell you whether a particular taxon is completely available or only partially available in BTK. A fully green line means all genomes under that taxa are available in BTK Viewer. A partial green line means only some of the genomes are available, and a black line or no line means that none of those genomes are available in BTK viewer. Click on Didymella arachidicola, which has a green underline indicating that a BTK view is available for it.

The taxonomy tree browser is useful because it lets you see at a glance how many species are available in the public archives, and how many have BTK views available.

2.Search based

Type the name of the species in the box and press enter. If you enter a partial name or a spelling mistake, you can pick one of the auto-complete suggestions (see the screen shot below). Here we typed “Didymella arachidicola” and the results will show a table with several columns which can be used to sort/filter the results. We will explore later in the course how to use these to explore ALL available datasets for contamination / co-bionts rapidly. For now, just click on the row with the species of interest which will take you straight to the BTK view for that assembly.

Click to expand,

The search box is easier to use if you already know the scientific name of the taxon you are interested in.

If, for some reason, you were not able to browse to the Didymella arachidicola BTK view or type it in the search box, you can also click on https://blobtoolkit.genomehubs.org/view/Didymella/dataset/WOCF01/blob#Filters

Both of the approaches above should have led you to this page. Which way do you prefer?